The present invention relates to methods and compositions for the detection, diagnosis, prevention and treatment of disease states and related disorders. The disease states of the present invention include cardiac, kidney and inflammatory disease. Specifically, genes that are differentially expressed in the cells, tissues, or peripheral blood of a subject suffering from, or predisposed to, such disease states may be identified through the methods of the present invention.
The present invention also relates to compositions and methods useful in the diagnosis, prevention and therapeutic treatment of disease states through the use of the differentially expressed genes of the present invention. Methods and compositions are provided for the diagnostic evaluation and prognosis of conditions involving such disease states, for the identification of subjects exhibiting a predisposition to such conditions, for therapeutic uses, e.g., modulating the effect of such differentially expressed genes, for monitoring subjects undergoing clinical evaluation for the prevention and treatment of a disease and its disorders, and for monitoring the efficacy of compounds used in clinical trials.
The present invention relates generally to methods and compositions for the detection, diagnosis, prevention and treatment of a disease, specifically cardiac, kidney or inflammatory disease, and related disorders. Particularly, the present invention relates to methods useful in diagnosing, identifying, monitoring, preventing, and treating the onset and progression of such disease states through the use of genes and gene products differentially expressed in a disease, specifically cardiac, kidney or inflammatory disease, along with modulators thereof.
By way of example, congestive heart failure (CHF) is a major cardiac disease associated with extensive morbidity and mortality. Traditionally, CHF has been treated by a series of agents including diuretics, vasodilators, angiotensin converting enzyme inhibitors, xcex2-adrenergic antagonists, and positive inotropes like digoxin. These drugs, however, principally provide symptomatic relief and typically only extend the life of one suffering from the disease for periods ranging from 6-12 months.
In response to hormonal, physiological, hemodynamic and pathological stimuli, adult ventricular muscle cells can adapt to increased workloads through the activation of a hypertrophic process. This process is characterized by an increase in the contractile protein content of cardiac muscle cells without a proliferative response because the adult cardiomyocyte is terminally differentiated and has lost its ability to divide. Cardiac growth during the hypertrophic process therefore results primarily from an increase in protein content per individual cardiomyocyte, with little or no change in cell number. The acquisition of the cardiac hypertrophic phenotype is in part dependent upon the activation of cardiac muscle gene program.
In addition to the induction of specific contractile protein components ventricular hypertrophy is also characterized by alterations in the expression of certain non-contractile proteins, such as atrial natriuretic peptide (ANP, also known as ANF). During embryonic development, the ANP gene is expressed in both the atrium and the ventricle. However, shortly after birth ANP expression is down regulated in the ventricle and expression is mainly confined to the atrium. Following induction of hypertrophy, ANP is reexpressed in the ventriculum. Thus, ANP expression can be considered to be a non-contractile protein marker of cardiac ventricular hypertrophy.
Ventricular hypertrophy is initially a compensatory mechanism by which the heart is attempting to counteract the effects of conditions like pressure overload, loss of contractile tissue, obstruction of blood flow, or increased peripheral demand for blood flow, all of which can be generated by a variety of physiological or pathological stimuli. In some circumstances, such as, injury or functional compromise of the heart, a typically short term, compensated hypertrophic response is desirable. Similarly, cardiac, e.g. left ventricular, hypertrophy (physiological hypertrophy) is often observed in some highly trained athletes, without any apparent cardiovascular complications. However, under some circumstances the hypertrophic response may eventually contribute to cardiac dysfunction. These circumstances include, but are not limited to, excessive hypertrophy, prolonged hypertrophy, or hypertrophy occurring in the context of toxic factors or toxic concentrations of factors that, when combined with the hypertrophic response of cardiac myocytes, result in mechanical dysfunction, electrical conduction dysfunction, loss of cardiac wall elasticity, or stimulation of fibrosis. In these cases hypertrophy is termed decompensated hypertrophy, and antagonism of cardiac hypertrophy is considered desirable. Once the transition from compensated to decompensated hypertrophy is achieved, the progression to a terminal heart failure phenotype often rapidly follows.
Heart failure affects approximately five million Americans. New cases of heart failure number about 400,000 each year. The pathophysiology of CHF is rather complex. Generally, the central hallmark of the disease is the inability of the heart to pump sufficient oxygenated blood to meet the demands of peripheral tissues. Numerous etiologies contribute to the development of CHF, including primary diseases of, or insults to, the myocardium itself, cardiac defects, hypertension, inflammation, kidney disease and vascular disease. These conditions lead to the hypertrophy and remodeling of the cardiac ventricles which, if unchecked, ultimately reduce the mechanical performance of the heart. Forces associated with the inability of the heart to pump blood ultimately lead to the release of neurohormones like catecholamines, renin-angiotensin, aldosterone, endothelin and related factors into the circulation. It has been demonstrated that elevations in plasma levels of many of these circulating neurohormones have a deleterious impact on the outcome of patients with CHF. Local production of these neurohormonal factors in the heart is believed to contribute centrally to the disease. Thus, an important therapeutic strategy has been to block this neurohormonal axis contributing to the pathogenesis of this disease.
Factors known to contribute centrally to the pathophysiology of heart disease are biosynthesized in the heart itself. These factors are produced in cardiac myocytes, fibroblasts, smooth muscle and endothelial cells, and inflammatory cells associated with the myocardium. For example, the heart has been shown to contain its own renin-angiotensin system. Blockade of the cardiac renin-angiotensin system is believed to contribute significantly to the therapeutic efficacy of the therapeutic class of agents known as angiotensin converting enzyme (ACE) inhibitors.
The heart also produces other factors including, but not limited to, endothelins, bradykinin, adrenomedullin, tumor necrosis factor, transforming growth factors, and natriuretic peptides. Unfortunately, therapeutic strategies are limited to the modulation of such substances, which are already known to contribute to the disease. Indeed, it is estimated that the functional contributions of only a minor fraction of all known secreted factors encoded by the human genome have been defined. Thus, it would be beneficial to discover differentially expressed genes related to disease states, in addition to methods and compositions for the diagnostic evaluation and prognosis of conditions involving such diseases, for the identification of subjects exhibiting a predisposition to such conditions, for modulating the effect of these differentially expressed genes and their expression products, for monitoring patients undergoing clinical evaluation for the prevention and treatment of a disease, specifically cardiac, kidney or inflammatory disease, and its disorders, and for monitoring the efficacy of compounds used in clinical trials. There is a particularly great interest in trying to understand the mechanisms which induce and control ventricular hypertrophy and indeed to dissect the transition from compensated to decompensated hypertrophy.
Recent observations, for example, show that the expression of genes encoding the natriuretic peptides, Atrial Natriuretic Peptide (xe2x80x9cANPxe2x80x9d) and Brain Natriuretic Peptide (xe2x80x9cBNPxe2x80x9d), which are believed to play important cardioprotective roles in CHF, is markedly up regulated (i.e., differentially expressed) in association with the progression of CHF in animal models and humans. Levels of messenger RNAs encoding endothelin, angiotensin converting enzyme, transforming growth factor and its receptors, and adrenomedullin are all changed during the progression of cardiac disease. Indeed, the differential expression of a gene in association with a disease implicates the gene as playing a key role in the progression of the disease itself. Accordingly, a strategy aimed at the identification of genes which are differentially expressed in association with a disease, specifically cardiac, kidney or inflammatory disease, will likely elucidate expression products or other factors that can contribute to or ameliorate the symptoms of the disease state and are potential candidate targets for therapeutic modulation or which are potentially therapeutic themselves. Such genes can also contribute to methodologies for diagnosing, evaluating, preventing and treating such diseases.
The primary goal of therapy for cardiac diseases has been the relief of symptoms associated with reduced cardiac output. Although current drugs provide some improvement in cardiac output, they fail to address the underlying mechanisms that lead to heart failure. A lack of understanding of the mechanisms responsible for progressive heart failure has made it difficult to devise long term strategies for treatment. Recently, investigators have begun to examine the underlying biology of the failing heart by examining the changes in gene expression that coincide with disease progression, however, the ability to comprehensively examine gene regulation in congestive heart failure has been technologically restricted. Understanding the fundamentals of heart disease should aid in the development of new drugs which not only improve cardiac function acutely, but also lead to improvements in long term survival. This holds true for other diseases as well.
Patients with symptomatic heart failure present with shortness of breath, edema, and extreme fatigue, often leading to death. The transition to end-stage failure can occur shortly or long after initial damage. To compensate for increased load due to damage, the left ventricle undergoes a hypertrophic response, characterized by increases in size of the cardiomyocyte without cell proliferation. In addition to changes in mass, the heart tissue also remodels the cellular architecture of the cardiomyocyte, evident as alterations in sarcomeric structure and contractile fiber formation. Following initial compensatory changes, the myocardium can ultimately fail due to irreversible enlargement and dilation. To afford the cellular changes in the tissues of the remodeling heart, there are many documented molecular changes, which are controlled by changes in cardiac gene expression (Komuro el al., Ann. Rev. Physiol. 55:55-75 (1993)). Such changes are not, however, confined to the cardiac myocyte. As important are the alterations and remodeling of the interstitial compartment. For example, proliferation and activation of cardiac myocytes in the failing heart lead to extracellular matrix deposition, which negatively affects the contractility of the ventricle wall.
Many studies, which examine molecular and cellular changes in various diseases, have been conducted using animal models of disease states. In one model, surgical placement of a steel band around the ascending aorta causes pressure overload on the heart (Schunkert et al., J. Clin. Invest. 86(6):1913-20 (1990)). To compensate for the increase in pressure due to the aortic constriction, the left ventricle increases in mass via cellular hypertrophy of the cardiacmyocyte. Left ventricular hypertrophy (LVH) displayed in the banded rat is strikingly similar to human heart disease associated with hypertension or valvular disease, which expose the myocardium to prolonged pressure overload. Continued pressure overload in the rat model of LVH ultimately leads to heart failure. This represents a recapitulation of the chronic hypertensive condition observed in humans. As in humans, a compensated hypertrophic heart can maintain diastolic and systolic function, but eventually the LVH response is exhausted, and continued cell loss and fibrosis leads to a demise of the heart. The rat LVH model is well suited to examine cellular and molecular changes associated with early responses to pressure overload, long term compensation, and late stage failure.
Several groups have exploited the rat LYH model to study gene expression related to heart disease. Within an hour of pressure induction, a change in mRNA levels for certain growth response genes such as c-fos, c-myc, and hsp70 has been observed (Izumo et al., Proc. Natl. Acad. Sci. USA 85(2):339-43 (1988)). Induction of hypertrophy in rats responding to chronic pressure overload for 8-12 weeks is accompanied by a shift in expression of several genes from adult to fetal isoforms. This period of time is characterized by remodeling of the myofibrillary composition of the cardiomyocyte in the left ventricle. During this cellular transition, expression of adult myosin heavy chain, cardiac actin, and tropomyosin is replaced by that of isoforms typically expressed in the developing fetus (Izumo et al., supra). Others have shown that the natriuretic hormones ANP (Mercadier et al., Am. J. Physiol. 257(3 Pt. 2):H979-87 (1989)) and BNP (Hama et al., Circulation 92(6):1558-64 (1995)), and their corresponding mRNAs, are elevated in hypertrophic rat myocardium as seen in human heart disease. In addition, it has been shown that mRNA levels of calcium ATPase and phospholamban decrease (Komuro et al., supra), and angiotensin converting ACE enzyme (Schunkert et al., J. Clin. Invest. 96(6):2768-74 (1995)) mRNA levels increase in LVH.
Although the numerous findings on the changes in gene expression in disease are enlightening, the story is certainly incomplete. Most published works in this field have concentrated on expression analysis of a limited number of genes. For example, fewer than 100 genes have been evaluated for transcriptional control in cardiac hypertrophy, representing a small fraction of all genes expressed in the heart. It is anticipated that expression of hundreds of genes are altered in the failing heart, and their discovery could reveal additional information about fundamental aspects of cardiac biology and how the heart responds to chronic pressure overload.
Techniques have been developed to efficiently analyze the level of expression of specific genes in cells and tissues. These techniques include, but are not limited to, quantitative PCR, RNA diagnosticing, SAGE (sequential analysis of gene expression), differential display, and microarrays. The application of these techniques affords a most powerful analysis of gene expression, substantially more efficient than older methods used for this purpose. A particularly attractive method for assessing gene expression is the DNA microarray technique. In this method, nucleotide sequences of interest are plated, or arrayed, on a microchip substrate. The arrayed sequences are then hybridized with specific DNA probes from cells or tissues of interest.
A particularly important application of the microarray method allows for the assessment of differential gene expression in pairs of mRNA samples from two different tissues, or in the same tissue comparing normal versus disease states or time progression of the disease. Microarray analysis allows one to analyze the expression of known genes of interest, or for the discovery of novel genes expressed differentially in tissue pairs of interest. Thus, an attractive application of this technology is as a fundamental discovery tool to identify new genes, and their corresponding expression products, which contribute to the pathogenesis of disease and related conditions.
Microarray technology has been successfully applied to large-scale analysis of human gene expression to identify cancer-specific genes and inflammatory-specific genes (DeRisi et al., Nat. Genet. 14(4):457-60 (1996); Heller et al., Proc. Natl. Acad. Sci. USA 94(6):2150-55 (1997)). DeRisi et al. examined a pre-selected set of 870 different genes for their expression in a melanoma cell line and a non-tumorigenic version of the same cell line. The microarray analysis revealed a decrease in expression for 15/870 (1.7%) and an increase in expression for 63/870 (7.3%) of the genes in non-tumorigenic relative to tumorigenic cells (only signals  less than 0.52 or  greater than 2.4 were deemed significant). Heller et al. employed microarrays to evaluate the expression of 1000 genes in cells taken from normal and inflamed human tissues. The results indicated that altered expression was evident in genes encoding inflammatory mediators such as IL-3, and a tissue metalloprotease. These results demonstrate the utility of applying microarray technology to complex human diseases, as described in detail supra.
In one embodiment of the present invention, genes, which are differentially expressed in association with a disease, specifically cardiac, kidney or inflammatory disease, are identified using the methods of the present invention. In a preferred embodiment, DNA microarrays are utilized to identify the genes of the present invention. The present invention emphasizes the importance of gene regulation in association with a disease, specifically cardiac, kidney or inflammatory disease. One skilled in the art, in view of the present disclosure, recognizes that the expression products of these genes have application as therapeutic agents, or targets for therapeutic modulation in a disease and its related conditions. The present invention also relates to the use of these genes, their expression products, and their modulators, in the detection, diagnosis, prevention, and treatment of disease.
Specifically, the present invention addresses deficiencies in the prior art by providing methods for identifying specific genes that are differentially expressed in subjects in response to a disease, specifically a cardiac, kidney or inflammatory disease, state, at a different level than such genes are expressed in a biological sample (e.g., cells, tissue or peripheral blood) obtained from a normal subject (i.e., a subject who is not suffering from or predisposed to the disease, e.g., a control subject). In a preferred embodiment, a disease state associated with the differentially expressed genes of the present invention may be detected, or diagnosed, by examining a blood sample rather than relying on a more invasive or less sensitive test to derive a prognosis. In addition, a subject may be monitored for disease progression, status, and response to therapies through monitoring of the expression of differentially expressed genes. Within the context of the present invention a xe2x80x9cpatient,xe2x80x9d xe2x80x9cindividual,xe2x80x9d or xe2x80x9csubjectxe2x80x9d are interchangeable terms and may be an animal, including a laboratory animal or other animal species, or a human.
As demonstrated herein, certain differentially expressed genes and methods of identifying such genes have been applied for the detection and treatment of a disease, specifically cardiac, kidney or inflammatory disease, and related conditions. Such cardiac diseases include CHF, dilated congestive cardiomyopathy, hypertrophic cardiomyopathy, restrictive cardiomyopathy, mitral valve disease, aortic valve disease, tricuspid valve disease, angina pectoris, myocardial infarction, cardiac arrhythmia, pulmonary hypertension, arterial hypertension, renovascular hypertension, arteriosclerosis, atherosclerosis, and cardiac tumors. Such kidney diseases include acute renal failure, glomerulonephritis, chronic renal failure, azotemia, uremia, immune renal disease; acute nephritic syndrome, rapidly progressive nephritic syndrome, nephrotic syndrome, Berger""s Disease, chronic nephritic/proteinuric syndrome, tubulointerstital disease, nephrotoxic disorders, renal infarction, atheroembolic renal disease, renal cortical necrosis, malignant nephroangiosclerosis, renal vein thrombosis, renal tubular acidosis, renal glucosuria, nephrogenic diabetes insipidus, Bartter""s Syndrome, Liddle""s Syndrome, polycystic renal disease, interstitial nephritis, acute hemolytic uremic syndrome, medullary cystic disease, medullary sponge kidney, hereditary nephritis, and nail-patella syndrome. Such inflammatory diseases include myocarditis, asthma, chronic inflammation, autoimmune diabetes, tumor angiogenesis, rheumatoid arthritis, rheumatoid spondylitis, osteoarthritis, gouty arthritis and other arthritic conditions, sepsis, septic shock, endotoxic shock, Gram-negative sepsis, toxic shock syndrome, asthma, adult respiratory distress syndrome, stroke, reperfusion injury, CNS injuries such as neural trauma and ischemia, psoriasis restenosis, cerebral malaria, chronic pulmonary inflammatory disease, silicosis, pulmonary sarcosis, bone resorption diseases such as osteoporosis, graft versus host reaction, Crohn""s Disease, ulcerative colitis including inflammatory bowel disease (IBD), and pyresis.
As a result of functional genomic studies, we have identified a number of genes that are differentially expressed in several animal models of cardiac, kidney and/or inflammatory diseases.
Accordingly, the present invention relates to methods and compositions for the detection, diagnosis, prevention, and treatment of a disease, specifically cardiac, kidney or inflammatory disease. Specifically, genes are identified and described which are differentially expressed in cells, tissue or peripheral blood relative to normal cells, tissue or peripheral blood and/or to cells, tissue or peripheral blood at a different stage of a disease, specifically cardiac, kidney or inflammatory disease. For example, genes are identified which are differentially expressed in subjects suffering from a disease, specifically cardiac, kidney or inflammatory disease, relative to normal subjects. The modulation of the expression of the identified genes and/or the activity of the identified gene products can be utilized therapeutically to prevent or treat a disease, specifically cardiac, kidney or inflammatory disease, and related disorders. As such, methods and compositions are described for the identification of novel therapeutic compounds for the inhibition of such diseases.
Further, the identified genes and/or gene products and/or modulators can be used to identify cells exhibiting or predisposed to a disorder involving a disease phenotype, thereby diagnosing individuals having, or at risk for developing, such disorders. Additionally, the identified genes and/or gene products can be used to determine severity or duration of such diseases. Furthermore, the detection of the differential expression of identified genes can be used to devise treatments for a disease, specifically cardiac, kidney or inflammatory disease. Still further, the detection of differential expression of identified genes can be used to design a preventive intervention for subjects at risk of such diseases.
One such method for the treatment of a disease, specifically cardiac, kidney or inflammatory disease, and most specifically cardiac disease, comprises the administration to a subject of an effective amount of a modulator of one or more genes encoding human proteins of the group consisting of native sequence 1-8U, native sequence prostacyclin-stimulating factor, native sequence osf-2, native sequence tissue specific mRNA protein, native sequence IGFBP-6, native sequence OSF-1, native sequence gas-1, native sequence YMP, native sequence BTG2, native sequence SDF1a, native sequence peripheral benzodiazepine receptor, and native sequence cellular ligand of annexin II. Another such method comprises the administration to a subject of an effective amount of a modulator of one or more human proteins of the group consisting of native sequence 1-8U, native sequence prostacyclin-stimulating factor, native sequence osf-2, native sequence tissue specific mRNA protein, native sequence IGFBP-6, native sequence OSF-1, native sequence gas-1, native sequence YMP, native sequence BTG2, native sequence SDF1a, native sequence peripheral benzodiazepine receptor, and native sequence cellular ligand of annexin II. The subject may preferably be a human patient.
This modulator may be positive or negative; consist of one or more human proteins of the group consisting of 1-8U, prostacyclin-stimulating factor, osf-2, tissue specific mRNA protein, IGFBP-6, OSF-1, gas-1, YMP, BTG2, SDF1a, peripheral benzodiazepine receptor, and cellular ligand of annexin II; and be selected from the group consisting of peptides, phosphopeptides, small organic or inorganic molecules, antibodies, and epitope-binding fragments. In addition, a modulator may be selected from the group consisting of antisense, ribozyme, and triple helix molecules.
Yet another such method for the treatment of a disease, specifically cardiac, kidney or inflammatory disease, and most specifically cardiac disease, comprises the administration to a human patient of an effective amount of one or more isolated human proteins of the group consisting of native sequence 1-8U, native sequence prostacyclin-stimulating factor, native sequence osf-2, native sequence tissue specific mRNA protein, native sequence IGFBP-6, native sequence OSF-1, native sequence gas-1, native sequence YMP, native sequence BTG2, native sequence SDF1a, native sequence peripheral benzodiazepine receptor, and native sequence cellular ligand of annexin II. Further methods of the present invention comprise the administration to a human patient of an effective dose of an antibody to a cellular receptor of, an organic molecule inhibitor capable of binding to a cellular receptor of, an expression product of an isolated nucleotide sequence encoding, or a syngeneic host cell transformed with an isolated nucleotide sequence encoding one or more human proteins.
This isolated nucleotide sequence may comprise an antisense oligonucleotide capable of hybridizing with, and inhibiting the translation of, the mRNA encoded by a gene encoding one or more of the human proteins of the group consisting of 1-8U, prostacyclin-stimulating factor, osf-2, tissue specific mRNA protein, IGFBP-6, OSF-1, gas-1, YMP, BTG2, SDF1a, peripheral benzodiazepine receptor, and cellular ligand of annexin II. Further embodiments of the present invention may use this DNA molecule as a vector or operably linked to a regulatory sequence that controls expression of the coding sequence in a host cell, said host cell preferably comprising a human cell such as a cardiac cell, more preferably a left ventricle cell.
Another embodiment of the present invention provides for the screening of a subject suspected of having a disease, specifically cardiac, kidney, or inflammatory disease, and more specifically cardiac disease. The expression of one or more proteins selected from the group consisting of 1-8U, prostacyclin-stimulating factor, osf-2, tissue specific mRNA protein, IGFBP-6, OSF-1, gas-1, YMP, BTG2, SDF1a, peripheral benzodiazepine receptor, and cellular ligand of annexin II is determined in a subject suspected of having, or being predisposed to, a cardiac disease, and compared to the expression levels of the one or more proteins in a normal subject. Further, this difference in expression is preferably at least about two-fold or more in the subject, and the subject is preferably a human patient.
In another embodiment, an array comprising one or more oligonucleotides complementary to reference DNA or RNA sequences encoding one or more human proteins selected from the group consisting of 1-8U, prostacyclin-stimulating factor, osf-2, tissue specific mRNA protein, IGFBP-6, OSF-1, gas-1, YMP, BTG2, SDF1a, peripheral benzodiazepine receptor, and cellular ligand of annexin II is used for detecting disease, specifically cardiac, kidney, or inflammatory disease. The reference DNA or RNA preferably is obtained from a biological sample from a normal subject and from a subject exhibiting a disease, specifically cardiac, disease. Such subjects are preferably humans. The biological sample preferably comprises peripheral blood or tissue, preferably a cell such as a cardiac cell, and more preferably a left ventricle cell.
Yet another embodiment of the present invention provides for diagnosing a disease, specifically cardiac, kidney, or inflammatory disease, and more specifically cardiac disease, in a human patient. The expression level of one or more proteins selected from the group consisting of 1-8U, prostacyclin-stimulating factor, osf-2, tissue specific mRNA protein, IGFBP-6, OSF-1, gas-1, YMP, BTG2, SDF1a, peripheral benzodiazepine receptor, and cellular ligand of annexin II is determined in the subject and compared to the expression levels of the one or more proteins in a normal subject. Such subjects are preferably humans. Further, this difference in expression is preferably at least about two-fold or more. A tissue sample from the human patient may be obtained from cardiac tissue, specifically left ventricle tissue, or from the subject""s blood. cDNA probes are hybridized on the array to create fluorometric, colorimetric or such identifying emissions, which are then compared with the existing encoded proteins.
Further, a diagnostic kit comprising said array is contemplated and used for detecting and diagnosing a disease, specifically cardiac, kidney or inflammatory disease. This kit may comprise control oligonucleotide probes, PCR reagents and detectable labels. In addition, this kit may comprise biological samples taken from human subjects, said samples comprising blood or tissue, preferably cardiac tissue, more preferably left ventricle cells. Such diagnostic kits may also comprise antibodies to the differentially expressed disease state genes of the present invention, which may be monoclonal.
In still another embodiment of the present invention, a method is provided for identifying a modulator of a differentially expressed disease state gene comprising contacting a biological sample from a subject having a disease, specifically cardiac, kidney or inflammatory disease, with a compound and determining the expression level of said differentially expressed gene. Comparison may be made between the expression level of the differentially expressed gene in a normal subject or said subject prior to contact with a compound and the expression level of the differentially expressed gene after contact with a compound, said compound selected from the group consisting of small molecules, active polypeptides and antibodies.